Abstract
BackgroundMicroRNAs (miRNAs) are small, non-coding RNAs that regulate protein levels post-transcriptionally. miRNAs play important regulatory roles in many cellular processes and have been implicated in several diseases. Recent studies have reported significant levels of miRNAs in a variety of body fluids, raising the possibility that miRNAs could serve as useful biomarkers. Next-generation sequencing (NGS) is increasingly employed in biomedical investigations. Although concordance between this platform and qRT-PCR based assays has been reported in high quality specimens, information is lacking on comparisons in biofluids especially urine. Here we describe the changes in miRNA expression patterns in a rodent model of renal tubular injury (gentamicin). Our aim is to compare RNA sequencing and qPCR based miRNA profiling in urine specimen from control and rats with confirmed tubular injury.ResultsOur preliminary examination of the concordance between miRNA-seq and qRT-PCR in urine specimen suggests minimal agreement between platforms probably due to the differences in sensitivity. Our results suggest that although miRNA-seq has superior specificity, it may not detect low abundant miRNAs in urine samples. Specifically, miRNA-seq did not detect some sequences which were identified by qRT-PCR. On the other hand, the qRT-PCR analysis was not able to detect the miRNA isoforms, which made up the majority of miRNA changes detected by NGS.ConclusionsTo our knowledge, this is the first time that miRNA profiling platforms including NGS have been compared in urine specimen. miRNAs identified by both platforms, let-7d, miR-203, and miR-320, may potentially serve as promising novel urinary biomarkers for drug induced renal tubular epithelial injury.
Highlights
MicroRNAs are small, non-coding RNAs that regulate protein levels post-transcriptionally. miRNAs play important regulatory roles in many cellular processes and have been implicated in several diseases
MiRNAs are readily quantified in serum, plasma and other body fluids, and more investigations are being directed to characterizing their potential as biomarkers
Histopathology and urinary protein biomarker data indicate gentamicin induced tubular injury at D7 with 50 mg/kg In order to characterize the miRNA changes that could be used as biomarkers of acute renal tubular injury, a study was conducted in the context of the Health and Environmental Sciences Institute (HESI) committee on Biomarkers of Nephrotoxicity in a well-established rat gentamicin toxicity model
Summary
MicroRNAs (miRNAs) are small, non-coding RNAs that regulate protein levels post-transcriptionally. miRNAs play important regulatory roles in many cellular processes and have been implicated in several diseases. Next-generation sequencing (NGS) is increasingly employed in biomedical investigations Concordance between this platform and qRT-PCR based assays has been reported in high quality specimens, information is lacking on comparisons in biofluids especially urine. Our aim is to compare RNA sequencing and qPCR based miRNA profiling in urine specimen from control and rats with confirmed tubular injury. There is a growing interest in the role of micro Ribonucleic Acids (miRNAs) in the pathogenesis of renal diseases [4,5] and a growing number of investigations are directed to characterizing their potential as biomarkers [6,7,8,9]. MiRNAs are highly conserved, endogenous, small (19–25 nucleotides), non-coding RNAs, with the primary fluids, and more investigations are being directed to characterizing their potential as biomarkers. NGS platform has been shown to generate highly reproducible, accurate data with high correlation to other platforms for high quality RNA samples [21,22,23,24], comparative data on media with low quality and quantity RNA are lacking
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